Zmays Zm00001d027536
From GreeNC
This table contains information about coordinates, assembly and annotation regarding the lncRNA-transcribing gene. In details, it shows whether this this gene transcribes any protein-coding transcript.
| Gene alias / name | Chrom. | Start | End | Assembly | Species | Details
|
|---|---|---|---|---|---|---|
| Zmays_Zm00001d027536 [ Zm00001d027536] |
1 | 7686285 | 7701265 | v4 | Zea mays (Phytozome 13) | Coding? Yes |
This table shows how a lncRNA has been classified (high/low confidence) or whether it has been classified as pre-miRNA (go to FAQ for classification criteria). Besides, it displays the lncRNA length and sequence as well as information about the ORF, the coding potential calculated by the Coding Potential Calculator (CPC), and the folding energies calculated by RNAfold.
| Transcript alias / name | Confidence | Pre-miRNA | Length | Orthologous group | Sequence | Details
|
|---|---|---|---|---|---|---|
| Zmays_Zm00001d027536_T001 Zm00001d027536_T001 |
Low | Yes | 2797 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.135 Folding energies... MFEI: -28.005 AMFE: -0.725 GC content %: 38.613 | |
| Zmays_Zm00001d027536_T004 Zm00001d027536_T004 |
Low | Yes | 2385 | [2] | Get ORF Coding potential... Type: noncoding Potential: -0.080 Folding energies... MFEI: -28.021 AMFE: -0.709 GC content %: 39.539 |
The lncRNAs from GreeNC have been analysed against the following databases: SwissProt, miRBase, Rfam, RepBase (RepeatMasker), NONCODE, and lncRNAdb. This table displays any association with these databases.
| Transcript alias | Database | Version | Hit | Evalue |
|---|---|---|---|---|
| Zmays_Zm00001d027536_T004 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Gypsy | |
| Zmays_Zm00001d027536_T001 | SwissProt | 2021-04-01 | Q10S58 | 1.59e-13 |
| Zmays_Zm00001d027536_T004 | SwissProt | 2021-04-01 | Q10S58 | 1.27e-13 |
| Zmays_Zm00001d027536_T001 | Rfam | 14.6 | MIR477 | 1.2e-5 |
| Zmays_Zm00001d027536_T004 | Rfam | 14.6 | MIR477 | 1.0e-5 |
| Zmays_Zm00001d027536_T001 | RepBase (RepeatMasker) | 0000-00-00 | LTR/Gypsy |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
